UPDATE:
So this is interesting. I reported earlier that the issue appeared to be solved when using WD Green drives in Voyager Q docks, and it is for the GREEN drives, which is DIFFERENT behavior from 10.9.0 and 10.9.2. The WD Green drives DO go to sleep now when their built in trigger tells them to, like everyone else, they did NOT sleep in .0 and .1. Then other posts today from people saying it didn't fix anything got me thinking, so I pulled other drives to test in the dock. A Seagate Barracuda 7200.13 drive and WD Black.
These drives are NOT power-saving drives like the Greens and lo and behold, same problem as before, they keep spinning and do not sleep even if Energy settings are set to do so, and they stay spinning even after shutdown.
My apologies for getting people's hopes up. I should have tested other drives besides the Greens. Whether by design or unintentionally, SOMETHING changed in .2, as the Greens are working as expected. Based on Lcrooks conversation with the AE, it looks like it was unintentional